NM_000287.4(PEX6):c.1802G>A (p.Arg601Gln) AND multiple conditions

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 18, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000850505.4

Allele description [Variation Report for NM_000287.4(PEX6):c.1802G>A (p.Arg601Gln)]

NM_000287.4(PEX6):c.1802G>A (p.Arg601Gln)

Gene:

PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_000287.4(PEX6):c.1802G>A (p.Arg601Gln)

HGVS:

NC_000006.12:g.42967450C>T
NG_008370.1:g.16794G>A
NM_000287.4:c.1802G>AMANE SELECT
NM_001316313.2:c.1538G>A
NP_000278.3:p.Arg601Gln
NP_001303242.1:p.Arg513Gln
NC_000006.11:g.42935188C>T
NM_000287.3:c.1802G>A
NM_001316313.1:c.1538G>A
NR_133009.2:n.1833G>A
Q13608:p.Arg601Gln

Protein change:

R513Q; ARG601GLN

Links:

UniProtKB: Q13608#VAR_058383; OMIM: 601498.0012; dbSNP: rs34324426

NCBI 1000 Genomes Browser:

rs34324426

Molecular consequence:

NM_000287.4:c.1802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001316313.2:c.1538G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_133009.2:n.1833G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Peroxisome biogenesis disorder 4A (Zellweger) (PBD4A)
Synonyms:: Zellweger syndrome spectrum (PEX6-related)
Identifiers:: MONDO: MONDO:0013930; MedGen: C3553936; Orphanet: 912; OMIM: 614862

Name:: Peroxisome biogenesis disorder 4B (PBD4B)
Identifiers:: MONDO: MONDO:0013931; MedGen: C3553937; Orphanet: 44; OMIM: 614863

Name:: Heimler syndrome 2 (HMLR2)
Synonyms:: PEROXISOME BIOGENESIS DISORDER 4C
Identifiers:: MedGen: C4225267; Orphanet: 3220; OMIM: 616617

Recent activity

Clear Turn Off Turn On

ribonuclease 7 precursor [Homo sapiens]
ribonuclease 7 precursor [Homo sapiens]
gi|1519315756|ref|NP_115961.3|

Protein
C962R [African swine fever virus]
C962R [African swine fever virus]
gi|783806627|gb|AJZ77047.1|

Protein
AEP1 [Saccharomyces cerevisiae]
AEP1 [Saccharomyces cerevisiae]
gi|3349|emb|CAA40367.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000992708	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 12, 2018)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 19105186, 26387595, 25079577, 25741868
SCV004803208	Institute of Immunology and Genetics Kaiserslautern	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 18, 2024)	paternal	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000992708

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 12, 2018)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004803208

Institute of Immunology and Genetics Kaiserslautern

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 18, 2024)

paternal

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.

Yik WY, Steinberg SJ, Moser AB, Moser HW, Hacia JG.

Hum Mutat. 2009 Mar;30(3):E467-80. doi: 10.1002/humu.20932.

PubMed [citation]

PMID:: 19105186
PMCID:: PMC2649967

Heimler Syndrome Is Caused by Hypomorphic Mutations in the Peroxisome-Biogenesis Genes PEX1 and PEX6.

Ratbi I, Falkenberg KD, Sommen M, Al-Sheqaih N, Guaoua S, Vandeweyer G, Urquhart JE, Chandler KE, Williams SG, Roberts NA, El Alloussi M, Black GC, Ferdinandusse S, Ramdi H, Heimler A, Fryer A, Lynch SA, Cooper N, Ong KR, Smith CE, Inglehearn CF, Mighell AJ, et al.

Am J Hum Genet. 2015 Oct 1;97(4):535-45. doi: 10.1016/j.ajhg.2015.08.011. Epub 2015 Sep 17.

PubMed [citation]

PMID:: 26387595
PMCID:: PMC4596894

See all PubMed Citations (4)

Details of each submission

From Baylor Genetics, SCV000992708.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute of Immunology and Genetics Kaiserslautern, SCV004803208.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

ACMG Criteria: PS3, PS4, PM3, PP3, PP5; Individual was compound heterozygous for PEX6 variants c.1314_1321del and c.1802G>A

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine